Keying by WAS common 50 years ago. For example, on the Flushing IRT nearly all the PM rush hour expresses I rode to Main Street (at the rail fan window) keyed by the red automatic signals on the down grade approaching the tunnel portal at Lawrence St (now College Pt Blvd). In this way they could make it to the first homing signal, which usually changed just before they got there. Also they had only 2 platform timers at Main St, and they were much faster than the current ones, allowing the trains to clear the switches faster. I also saw trains on the E and F frequently key by approaching stations in the rush hour. In this way, if the train ahead got delayed by a few seconds, they could make it up, minimizing a "domino" effect. As far as tripping trains, maybe it was because I brought the motormen bad luck, but it happened so often I stopped counting.
Your anecdotal evidence is contrary to my own experiences during the 1954-1959 period, when I too regularly rode both the Flushing and E/F lines.
I must confess that I too thought that the motormen passed red signals on their approach to Main St from looking out the front window. However, I'd also occasionally look out the front door during the winter months. I'd see that the aspect had changed just before the train moved from the color of the signal light's glow. Looking out the front window had obscured a clear view of the signal because the motormen pulled even with it. I could not see the aspect change because the train body blocked a view of the signal and the beam.
I have two explanations for today's backups into Main St. First, there tower operators were more attentive back then. Second, the clocks at the Main St and Times Sq dispatchers are not synchronized. The Main St clock is running slow compared to that at Times Sq. The result is that trains arrive at Main St sooner than they leave. It also means that trains at Times leave sooner than arriving trains - meaning that the platform is sometimes empty. There was always a train loading at Times Sq back in the '50s.
The E/F was a different story. I could invariably see a train in Roosevelt, Queens Plaza, Ely, Lex and 5th Ave when the train I was on started to approach. However, that train invariably started to leave as my train got closer to the station. Indeed, the aspect just changed to permit the train to enter the station by the time it arrived.
In any case, the signals control the safety of the system. The signals should not also control train schedules. They don't on manual systems that currently operate 35+ tph. They use schedule timers within each station that are independent of the signal system for that function.